Mar 26, 2024
Version 2
GeoMx Digital Spatial Profiler (DSP) Protocol v2 - University of Minnesota TMCs V.2
- Laura J Niedernhofer1,
- David A Bernlohr1
- 1University of Minnesota, Minneapolis, MN
- Cellular Senescence Network (SenNet) Method Development Community
Protocol Citation: Laura J Niedernhofer, David A Bernlohr 2024. GeoMx Digital Spatial Profiler (DSP) Protocol v2 - University of Minnesota TMCs. protocols.io https://dx.doi.org/10.17504/protocols.io.8epv5r7k6g1b/v2Version created by Allie Pybas
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: March 26, 2024
Last Modified: March 26, 2024
Protocol Integer ID: 97409
Funders Acknowledgements:
NIH
Grant ID: 5U54AG076041-03
NIH
Grant ID: 5U54AG079754-02
Abstract
The nanoString GeoMx‱ Digital Spatial Profiler (DSP) is a platform that allows high-plex profiling at the protein and RNA level, providing spatial and temporal assessment of tumors in frozen or formalin-fixed paraffin-embedded limited tissue sample.
The following protocols/manuals were used at the University of Minnesota TMCs in collaboration with the University of Minnesota Genomics Center.
Slide Preparation
Slide Preparation
GeoMx DSP Manual Slide Preparation User Manual
MAN-10150-04.pdf2.7MB ROI Acquisition
ROI Acquisition
GeoMx DSP Instrument User Manual
MAN-10152-04.pdf51.3MB Library Preparation
Library Preparation
GeoMx DSP NGS Readout User Manual
MAN-10153-04.pdf9.2MB Note
Sequence with the read format 27,8,8,27
FASTQ Generation
FASTQ Generation
BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq version 2.20.0